Off topic:ggplot2 returns empty plot
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5.1 years ago
zizigolu ★ 4.3k

Hi,

I am trying to determine copy number in tumor and normal sample, so I calculated depth and so on by mosdepth and I finished with this table

https://www.dropbox.com/s/11jlie6kufibg4y/all_depth.txt?dl=0

> head(all_depth)
      Chr Start Counts.100Tumor Counts.100Normal       diff
    1   1     0            0.00          0.00000   0.000000
    2   1 10000           55.21         69.75838 -14.548375
    3   1 20000           32.24         34.81226  -2.572259
    4   1 30000           33.36         36.21775  -2.857753
    5   1 40000           24.45         26.22632  -1.776319
    6   1 50000           35.73         34.33420   1.395800
    > 


ggplot(all_depth[all_depth$Chr == "chr6",], aes(x=Start, y=diff, color=diff)) + geom_point() + scale_color_viridis("Depth", option = "plasma")

I was going to plot that like this picture from tutorial

enter image description here

But R gives me an empty plot, do you know why? I don't know where I am doing wrong I even tried for all chromosomes

ggplot2 R software error CNV • 1.9k views
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